Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in...Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in cucumber have been identified.Here,the heat injury indices of 88 cucumber accessions representing diverse ecotypes were collected in two open-field environments,with naturally occurring high temperatures over two years.Seventeen of the 88 accessions were identified as highly heat-tolerant.Using a genome-wide association study,five loci(gHII3.1,gHII3.2,gHII3.3,gHII4.1 and gHII6.1)on three chromosomes associated with heat tolerance were detected.Pairwise linkage disequilibrium correlation,sequence polymorphisms,and qRT-PCR analyses at these loci,identified five candidate genes predicted to be casual for heat stress response in cucumber.CsaV3_3G04883,CsaV3_4G029050 and CsaV3_6G005370 each had nonsynonymous SNPs,and were significantly up-regulated by heat stress in the heat-tolerant genotypes.CsaV3_3G031890 was also induced by heat stress,but in the heatsensitive genotypes,and sequence polymorphism was only found in the promoter region.Identifying these candidate genes lays a foundation for understanding cucumber thermotolerance mechanisms.Our study is one of the few to examine heat stress in adult cucumber plants and it therefore fills a critical gap in knowledge.It is also an important first-step towards accelerating the breeding of robust heat-tolerant varieties.展开更多
Cucumber is one of the most widely consumed vegetables worldwide,and the fruit spine is an important fruit quality trait.Expansins play critical roles in fruit development;however,the regulation of expansins in cucumb...Cucumber is one of the most widely consumed vegetables worldwide,and the fruit spine is an important fruit quality trait.Expansins play critical roles in fruit development;however,the regulation of expansins in cucumber fruit spine development has not been reported.In this study,33 expansin genes were identified in the cucumber genome V3;additionally,expansin genes in Citrullus lanatus,Cucumis melo,Cucurbita maxima,Lagenaria siceraria,and Benincasa hispida were also identified.Phylogenetic analysis of expansin proteins in Cucurbitaceae and Arabidopsis showed that they evolved separately in each plant species.Phylogenetic analysis showed that C.maxima was derived earlier than the other five Cucurbitaceae species.The expression of CsEXPA2,CsEXPA14,and CsEXLA3 varied in cucumber lines with different fruit spine densities.A yeast two-hybrid assay showed that a putative auxin transporter encoded by numerous spine gene(ns)interacts with CsEXLA2,which may be involved in the development of the numerous spines in cucumber.These results provide novel insights into the expansins related to plant development and fruit spine development in cucumber.展开更多
Heterosis has historically been exploited in plants;however,its underlying genetic mechanisms and molecular basis remain elusive.In recent years,due to advances in molecular biotechnology at the genome,transcriptome,p...Heterosis has historically been exploited in plants;however,its underlying genetic mechanisms and molecular basis remain elusive.In recent years,due to advances in molecular biotechnology at the genome,transcriptome,proteome,and epigenome levels,the study of heterosis in vegetables has made significant progress.Here,we present an extensive literature review on the genetic and epigenetic regulation of heterosis in vegetables.We summarize six hypotheses to explain the mechanism by which genes regulate heterosis,improve upon a possible model of heterosis that is triggered by epigenetics,and analyze previous studies on quantitative trait locus effects and gene actions related to heterosis based on analyses of differential gene expression in vegetables.We also discuss the contributions of yield-related traits,including flower,fruit,and plant architecture traits,during heterosis development in vegetables(e.g.,cabbage,cucumber,and tomato).More importantly,we propose a comprehensive breeding strategy based on heterosis studies in vegetables and crop plants.The description of the strategy details how to obtain F_(1) hybrids that exhibit heterosis based on heterosis prediction,how to obtain elite lines based on molecular biotechnology,and how to maintain heterosis by diploid seed breeding and the selection of hybrid simulation lines that are suitable for heterosis research and utilization in vegetables.Finally,we briefly provide suggestions and perspectives on the role of heterosis in the future of vegetable breeding.展开更多
Gummy stem blight(GSB),caused by Didymella bryoniae,is a serious fungal disease that leads to decline in cucumber yield and quality.The molecular mechanism of GSB resistance in cucumber remains unclear.Here,we investi...Gummy stem blight(GSB),caused by Didymella bryoniae,is a serious fungal disease that leads to decline in cucumber yield and quality.The molecular mechanism of GSB resistance in cucumber remains unclear.Here,we investigated the GSB resistance of cucumber core germplasms from four geographic groups at the seedling and adult stages.A total of 9 SNPs related to GSB resistance at the seedling stage and 26 SNPs at the adult stage were identified,of which some are co-localized to previously mapped Quantitative trait loci(QTLs)for GSB resistance(gsb3.2/gsb3.3,gsb5.1,and gsb-s6.2).Based on haplotype analysis and expression levels after inoculation,four candidate genes were identified within the region identified by both Genome-wide association study(GWAS)and previous identified QTL mapping,including Csa3G129470 for gsb3.2/gsb3.3,Csa5G606820 and Csa5G606850 for gsb5.1,and Csa6G079730 for gsb-s6.2.The novel GSB resistant accessions,significant SNPs,and candidate genes facilitate the breeding of GSB resistant cucumber cultivars and provide a novel idea for understanding GSB resistance mechanism in cucumber.展开更多
Dear Editor,Cucumber(Cucumis sativus)is a key vegetable crop and an essential model for genetics and genomics research in Cucurbitaceae,especially in studies on plant sex determination and vascular development.As the ...Dear Editor,Cucumber(Cucumis sativus)is a key vegetable crop and an essential model for genetics and genomics research in Cucurbitaceae,especially in studies on plant sex determination and vascular development.As the first sequenced genome among vegetable crops,the cucumber reference genome has been a crucial genetic resource for comparative genomics and genetic studies.However,the latest version of the cucumber cv.Chinese Long reference genome(CLv3.0),generated using PacBio long-reads data,is incomplete.Despite a predicted genome size of 350-367 Mb,CLv3.0 encompasses only 226.2 Mb,leaving 72 gaps and over 120 Mb of unknown sequences.This low assembly completeness(approximately 62%)is primarily due to the high proportion(~30%)of heterochromatic satellite and rDNA sequences in cucumber,substantially higher than that observed in many other species such as Arabidopsis,rice,maize,and watermelon,where it is less than 5%(Han et al.,2008;Huang et al.,2009;Li et al.,2019).展开更多
Low-temperature(LT)stress threatens cucumber production globally;however,the molecular mechanisms underlying LT tolerance in cucumber remain largely unknown.Here,using a genome-wide association study(GWAS),we found a ...Low-temperature(LT)stress threatens cucumber production globally;however,the molecular mechanisms underlying LT tolerance in cucumber remain largely unknown.Here,using a genome-wide association study(GWAS),we found a naturally occurring single nucleotide polymorphism(SNP)in the STAYGREEN(CsSGR)coding region at the gLTT5.1 locus associated with LT tolerance.Knockout mutants of CsSGR generated by clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease 9 exhibit enhanced LT tolerance,in particularly,increased chlorophyll(Chl)content and reduced reactive oxygen species(ROS)accumulation in response to LT.Moreover,the C-repeat Binding Factor 1(CsCBF1)transcription factor can directly activate the expression of CsSGR.We demonstrate that the LT-sensitive haplotype CsSGRHapA,but not the LT-tolerant haplotype CsSGR^(HapG)could interact with NON-YELLOW COLORING 1(CsNYC1)to mediate Chl degradation.Geographic distribution of the CsSGR haplotypes indicated that the CsSGR^(HapG)was selected in cucumber accessions from high latitudes,potentially contributing to LT tolerance during cucumber cold-adaptation in these regions.CsSGR mutants also showed enhanced tolerance to salinity,water deficit,and Pseudoperonospora cubensis,thus CsSGR is an elite target gene for breeding cucumber varieties with broad-spectrum stress tolerance.Collectively,our findings provide new insights into LT tolerance and will ultimately facilitate cucumber molecular breeding.展开更多
Fruit quality and yield are reduced when cucumber(Cucumis sativus L.)plants are exposed to low temperature(LT)stress,yet,the inheritance and genes linked to cold tolerance in adult plants have not been reported yet.He...Fruit quality and yield are reduced when cucumber(Cucumis sativus L.)plants are exposed to low temperature(LT)stress,yet,the inheritance and genes linked to cold tolerance in adult plants have not been reported yet.Here,the LTtolerance of 120 cucumber accessions representing four ecotypes were evaluated by GWAS,and also,in 140 recombinant inbred lines(RILs)derived from a biparental cross.Plants were exposed to naturally occurring LT environments in a plastic greenhouse,in winter 2022,and 2023,and a low temperature injury index(LTII)was employed to evaluate plant performance.Genetic analysis revealed that the LT-tolerance evaluated in the adult cucumber plants was a multigenic quantitative trait,and that 18 of the 120 accessions were highly LT tolerant by our LTII assessment.Two loci(gLTT1.1 and gLTT3.1)exhibited strong signals that were consistent and stable in two environments.In addition,two QTLs—qLTT1.2 on chromosome(Chr.)1,and qLTT3.1 on Chr.3,were discovered in all tests using RIL population derived from a cross between LT-sensitive‘CsIVF0106’,and LT-tolerant‘CsIVF0168’.qLTT1.2 was delimited to a 1.24-Mb region and qLTT3.1 was narrowed to a 1.43-Mb region.Interestingly,a peak single nucleotide polymorphism(SNP)at gLTT1.1 and gLTT3.1 was also found in qLTT1.2 and qLTT3.1,respectively.These loci were thus renamed as gLTT1.1 and gLTT3.1.In these regions,25 genes were associated with the LT response.By identifying differences in haplotypes and transcript profiles among these genes,we identified four candidates:CsaV3_1G012520(an ethylene-responsive transcription factor)and CsaV3_1G013060(a RING/U-box superfamily protein)in gLTT1.1,and two RING-type E3 ubiquitin transferases at CsaV3_3G018440 and CsaV3_3G017700 in gLTT3.1 that may regulate LT-tolerance in adult cucumber.Interestingly,the accessions in which the LT-tolerant haplotypes for two loci were pyramided,displayed maximally high tolerance for LT.These findings therefore provide a solid foundation for the identification of LT-tolerant genes and the molecular breeding of cucumber with LT-tolerance.展开更多
基金supported by Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding(Grant No.G20220628003-03)Chongqing Municipal People's Government and Chinese Academy of Agricultural Sciences strategic cooperation project,Key-Area Research and Development Program of Guangdong Province(Grant No.2020B020220001)+3 种基金the Earmarked Fund for Modern Agro-industry Technology Research System(Grant No.CARS-23)Science and Technology Innovation Program of the Chinese Academy of Agricultural Science(Grant No.CAAS-ASTIP-IVFCAAS)Central public-interest Scientific Institution Basal Research Fund(Grant No.Y2017PT52)the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture,P.R.China。
文摘Heat stress causes overgrowth,leaf dryness and fruit malformation,which negatively impacts cucumber quality and yield.Yet,in spite of the devastating consequences of this abiotic stress,few genes for heat tolerance in cucumber have been identified.Here,the heat injury indices of 88 cucumber accessions representing diverse ecotypes were collected in two open-field environments,with naturally occurring high temperatures over two years.Seventeen of the 88 accessions were identified as highly heat-tolerant.Using a genome-wide association study,five loci(gHII3.1,gHII3.2,gHII3.3,gHII4.1 and gHII6.1)on three chromosomes associated with heat tolerance were detected.Pairwise linkage disequilibrium correlation,sequence polymorphisms,and qRT-PCR analyses at these loci,identified five candidate genes predicted to be casual for heat stress response in cucumber.CsaV3_3G04883,CsaV3_4G029050 and CsaV3_6G005370 each had nonsynonymous SNPs,and were significantly up-regulated by heat stress in the heat-tolerant genotypes.CsaV3_3G031890 was also induced by heat stress,but in the heatsensitive genotypes,and sequence polymorphism was only found in the promoter region.Identifying these candidate genes lays a foundation for understanding cucumber thermotolerance mechanisms.Our study is one of the few to examine heat stress in adult cucumber plants and it therefore fills a critical gap in knowledge.It is also an important first-step towards accelerating the breeding of robust heat-tolerant varieties.
基金supported by the earmarked fund for Modern Agro-industry Technology Research System (CARS-23)the National Natural Science Foundation of China (31672172)+1 种基金The Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-IVFCAAS)the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture and Rural Affairs,China。
文摘Cucumber is one of the most widely consumed vegetables worldwide,and the fruit spine is an important fruit quality trait.Expansins play critical roles in fruit development;however,the regulation of expansins in cucumber fruit spine development has not been reported.In this study,33 expansin genes were identified in the cucumber genome V3;additionally,expansin genes in Citrullus lanatus,Cucumis melo,Cucurbita maxima,Lagenaria siceraria,and Benincasa hispida were also identified.Phylogenetic analysis of expansin proteins in Cucurbitaceae and Arabidopsis showed that they evolved separately in each plant species.Phylogenetic analysis showed that C.maxima was derived earlier than the other five Cucurbitaceae species.The expression of CsEXPA2,CsEXPA14,and CsEXLA3 varied in cucumber lines with different fruit spine densities.A yeast two-hybrid assay showed that a putative auxin transporter encoded by numerous spine gene(ns)interacts with CsEXLA2,which may be involved in the development of the numerous spines in cucumber.These results provide novel insights into the expansins related to plant development and fruit spine development in cucumber.
基金the National Key Research and Development Program of China[2016YFD0101705]the Earmarked Fund for Modern Agro–industry Technology Research System[CARS–25]the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture,China.
文摘Heterosis has historically been exploited in plants;however,its underlying genetic mechanisms and molecular basis remain elusive.In recent years,due to advances in molecular biotechnology at the genome,transcriptome,proteome,and epigenome levels,the study of heterosis in vegetables has made significant progress.Here,we present an extensive literature review on the genetic and epigenetic regulation of heterosis in vegetables.We summarize six hypotheses to explain the mechanism by which genes regulate heterosis,improve upon a possible model of heterosis that is triggered by epigenetics,and analyze previous studies on quantitative trait locus effects and gene actions related to heterosis based on analyses of differential gene expression in vegetables.We also discuss the contributions of yield-related traits,including flower,fruit,and plant architecture traits,during heterosis development in vegetables(e.g.,cabbage,cucumber,and tomato).More importantly,we propose a comprehensive breeding strategy based on heterosis studies in vegetables and crop plants.The description of the strategy details how to obtain F_(1) hybrids that exhibit heterosis based on heterosis prediction,how to obtain elite lines based on molecular biotechnology,and how to maintain heterosis by diploid seed breeding and the selection of hybrid simulation lines that are suitable for heterosis research and utilization in vegetables.Finally,we briefly provide suggestions and perspectives on the role of heterosis in the future of vegetable breeding.
基金supported by the Earmarked Fund for Modern Agro-industry Technology Research System(Grant No.CARS-23)the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(Grant No.CAASASTIP-IVFCAAS)the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture and Rural Affairs,P.R.China.
文摘Gummy stem blight(GSB),caused by Didymella bryoniae,is a serious fungal disease that leads to decline in cucumber yield and quality.The molecular mechanism of GSB resistance in cucumber remains unclear.Here,we investigated the GSB resistance of cucumber core germplasms from four geographic groups at the seedling and adult stages.A total of 9 SNPs related to GSB resistance at the seedling stage and 26 SNPs at the adult stage were identified,of which some are co-localized to previously mapped Quantitative trait loci(QTLs)for GSB resistance(gsb3.2/gsb3.3,gsb5.1,and gsb-s6.2).Based on haplotype analysis and expression levels after inoculation,four candidate genes were identified within the region identified by both Genome-wide association study(GWAS)and previous identified QTL mapping,including Csa3G129470 for gsb3.2/gsb3.3,Csa5G606820 and Csa5G606850 for gsb5.1,and Csa6G079730 for gsb-s6.2.The novel GSB resistant accessions,significant SNPs,and candidate genes facilitate the breeding of GSB resistant cucumber cultivars and provide a novel idea for understanding GSB resistance mechanism in cucumber.
基金the National Key Research and Development Program(grant no.2023YFD1201500)the Earmarked Fund for Modern Agro-industry Technology Research System(grant no.CARS-23)+1 种基金the Agricultural Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences(grant no.CAAS-ASTIP-2021-IVF)the Central Public-interest Scientific Institution Basal Research Fund(grant no.IVF-BRF2023005).
文摘Dear Editor,Cucumber(Cucumis sativus)is a key vegetable crop and an essential model for genetics and genomics research in Cucurbitaceae,especially in studies on plant sex determination and vascular development.As the first sequenced genome among vegetable crops,the cucumber reference genome has been a crucial genetic resource for comparative genomics and genetic studies.However,the latest version of the cucumber cv.Chinese Long reference genome(CLv3.0),generated using PacBio long-reads data,is incomplete.Despite a predicted genome size of 350-367 Mb,CLv3.0 encompasses only 226.2 Mb,leaving 72 gaps and over 120 Mb of unknown sequences.This low assembly completeness(approximately 62%)is primarily due to the high proportion(~30%)of heterochromatic satellite and rDNA sequences in cucumber,substantially higher than that observed in many other species such as Arabidopsis,rice,maize,and watermelon,where it is less than 5%(Han et al.,2008;Huang et al.,2009;Li et al.,2019).
基金supported by the National Natural Science Foundation of China (No. 32372704)Key-Area Research and Development Program of Guangdong Province (2020B020220001)+2 种基金Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding (G20220628003-03)the Earmarked Fund for Modern Agroindustry Technology Research System (CARS-23)Science and Technology Innovation Program of the Chinese Academy of Agricultural Science (CAAS-ASTIP-IVFCAAS)
文摘Low-temperature(LT)stress threatens cucumber production globally;however,the molecular mechanisms underlying LT tolerance in cucumber remain largely unknown.Here,using a genome-wide association study(GWAS),we found a naturally occurring single nucleotide polymorphism(SNP)in the STAYGREEN(CsSGR)coding region at the gLTT5.1 locus associated with LT tolerance.Knockout mutants of CsSGR generated by clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease 9 exhibit enhanced LT tolerance,in particularly,increased chlorophyll(Chl)content and reduced reactive oxygen species(ROS)accumulation in response to LT.Moreover,the C-repeat Binding Factor 1(CsCBF1)transcription factor can directly activate the expression of CsSGR.We demonstrate that the LT-sensitive haplotype CsSGRHapA,but not the LT-tolerant haplotype CsSGR^(HapG)could interact with NON-YELLOW COLORING 1(CsNYC1)to mediate Chl degradation.Geographic distribution of the CsSGR haplotypes indicated that the CsSGR^(HapG)was selected in cucumber accessions from high latitudes,potentially contributing to LT tolerance during cucumber cold-adaptation in these regions.CsSGR mutants also showed enhanced tolerance to salinity,water deficit,and Pseudoperonospora cubensis,thus CsSGR is an elite target gene for breeding cucumber varieties with broad-spectrum stress tolerance.Collectively,our findings provide new insights into LT tolerance and will ultimately facilitate cucumber molecular breeding.
基金supported by the National Natural Science Foundation of China(No.31902028)Key-Area Research and Development Program of Guangdong Province(2020B020220001)+4 种基金Beijing Joint Research Program for Germplasm Innovation and New Variety Breeding(G20220628003-03)Modern Agro-industry Technology Research System(CARS-23)Science and Technology Innovation Program of the Chinese Academy of Agricultural Science(CAAS-ASTIP-IVFCAAS)Central Public-interest Scientific Institution Basal Research Fund(Y2017PT52)the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops,Ministry of Agriculture,P.R.China.
文摘Fruit quality and yield are reduced when cucumber(Cucumis sativus L.)plants are exposed to low temperature(LT)stress,yet,the inheritance and genes linked to cold tolerance in adult plants have not been reported yet.Here,the LTtolerance of 120 cucumber accessions representing four ecotypes were evaluated by GWAS,and also,in 140 recombinant inbred lines(RILs)derived from a biparental cross.Plants were exposed to naturally occurring LT environments in a plastic greenhouse,in winter 2022,and 2023,and a low temperature injury index(LTII)was employed to evaluate plant performance.Genetic analysis revealed that the LT-tolerance evaluated in the adult cucumber plants was a multigenic quantitative trait,and that 18 of the 120 accessions were highly LT tolerant by our LTII assessment.Two loci(gLTT1.1 and gLTT3.1)exhibited strong signals that were consistent and stable in two environments.In addition,two QTLs—qLTT1.2 on chromosome(Chr.)1,and qLTT3.1 on Chr.3,were discovered in all tests using RIL population derived from a cross between LT-sensitive‘CsIVF0106’,and LT-tolerant‘CsIVF0168’.qLTT1.2 was delimited to a 1.24-Mb region and qLTT3.1 was narrowed to a 1.43-Mb region.Interestingly,a peak single nucleotide polymorphism(SNP)at gLTT1.1 and gLTT3.1 was also found in qLTT1.2 and qLTT3.1,respectively.These loci were thus renamed as gLTT1.1 and gLTT3.1.In these regions,25 genes were associated with the LT response.By identifying differences in haplotypes and transcript profiles among these genes,we identified four candidates:CsaV3_1G012520(an ethylene-responsive transcription factor)and CsaV3_1G013060(a RING/U-box superfamily protein)in gLTT1.1,and two RING-type E3 ubiquitin transferases at CsaV3_3G018440 and CsaV3_3G017700 in gLTT3.1 that may regulate LT-tolerance in adult cucumber.Interestingly,the accessions in which the LT-tolerant haplotypes for two loci were pyramided,displayed maximally high tolerance for LT.These findings therefore provide a solid foundation for the identification of LT-tolerant genes and the molecular breeding of cucumber with LT-tolerance.
